Dear mark <br><br><br>But how can it possible that starting structure is grossly broken , up to infltegro first step I enquired my structure It looks fine but after doing enegy minimisation step i saw that structure is disturbed <br>
May be its due to restrain not working on protein . To apply position restrain on protein I have edited posre.itp file with force constant 100000 and included it in topology file-<br> Include forcefield parameters<br>#include "ffG53a6_lipid.itp"<br>
<br>#include "topol_A.itp"<br>#ifdef POSRES<br>#include "posre_A.itp<br><br>#include "topol_B.itp<br>#ifdef POSRES<br>#include "posre_B.itp<br>#endif<br><br>But its not working .<br>I am unable to understand why?<br>
<br>can u give me some idea about that?<br><br>NITU sharma<br>